best pipeline/practice for analyzing WES for germline and somatic variant calling

Question

[epigene]

I haven't been doing variant calling for a long while and now I got a new project that I'll be doing some variant calling on cancer patient normal and tumor samples. I'm interested in calling both germline variants from the normal sample and somatic variants from the tumor/normal pair. I'm wondering if someone could share what's the latest best pipeline/practice for doing this type of work nowadays?

I was using GATK for germline and Mutect2 for somatic before.

Thanks!

Answer 1

[Pierre Lindenbaum]

https://nf-co.re/sarek

nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.

[epigene]

thanks for sharing! looks a new pipeline tool to learn..

[Pierre Lindenbaum]

new ? happy birthday nextflow :-)

The first Nextflow commit ^^ was pushed 10 years ago today! Many thanks to everyone in the community for joining us on the ride! #nextflow10https://t.co/AYT4EmmHbW pic.twitter.com/3QhxXMBcx1

— Nextflow (@nextflowio) March 22, 2023

[epigene]

i meant i've never used it myself.. :p

[epigene]

Pierre, could you please also recommend some well validated fastq file sets to test the pipeline and compare with other callers? I've known GIB but never used it. Would you recommend that? I'm looking for something small enough to handle on a local machine.